Neville's grandmother has sent him a Remembrall, a device to help him remember things. Draco attempts to steal it during breakfast, but Professor McGonagall's arrival interrupts him. At the flying lesson, Neville falls off his broom, injuring himself. The instructor, Madam Hooch, takes him to the hospital wing, ordering everyone else to remain on the ground. Spotting Neville's dropped Remembrall, Draco grabs it and takes off on his broom to place it in a tree for Neville to fetch later. Harry flies after him, discovering that he has a natural talent for flying on a broomstick. Draco, to avoid a mid-air conflict, hurls the Remembrall away, but Harry dives and catches it mid-air, just inches above the ground. He is immediately accosted by Professor McGonagall, who has been watching from her office. She drags him away, apparently in disgrace, but to his surprise introduces him to the Gryffindor Quidditch team captain, Oliver Wood, saying Harry is the new Seeker.

Later, surprised that Harry has avoided being expelled, Draco challenges him to a Wizard's Duel in the trophy room at midnight. Harry accepts, and Ron volunteers to be his second. As Harry and Ron sneak out later that night, circumstance adds Neville and Hermione to the party, though both Harry and Ron are unhappy that they are tagging along. Hermione, particularly, is unwelcome, as she keeps nagging Harry and Ron in an attempt to prevent the duel. Reaching the trophy room, they hear Filch approaching. Evidently Draco never intended to show up, but instead informed Filch that students would be there after hours. Peeves sees the students sneaking away, and yells that students are out of bed. The students run off, diving into the forbidden third-floor corridor. They evade Filch, but find their hiding place is occupied by a huge, ferocious three-headed dog. They escape back to the common room, where Hermione mentions that the dog was atop a trap door, apparently guarding something. Harry concludes the dog must be guarding the same package Hagrid retrieved from Gringotts Bank.

This is among the happiest chapters, at least initially, in Harry's early school career. We saw how he felt displaced – apart from the natural dislocation he feels being in a new school and a strange new world, Harry copes with sudden celebrity, and the associated ongoing feeling that he is somewhat a fraud. This is compounded by his seeming inability to perform magic with the same natural fluidity that many of his peers demonstrate, such as Hermione, who seems to know anything that can be learned from a book, while Harry muddles along. Harry is also concerned that his years among Muggles, particularly those Muggles, may have crippled his magical abilities – most other students have had magical upbringings and come equipped with an understanding that he lacks. However, Harry seems to overlook that Hermione, and other students, also grew up in Muggle households, with no more magical background than he has; Hermione, who has a stable home life, may just be more confident, plus she is an avid book learner, giving her a greater initiative and confidence to use her abilities than Harry.

Imagine Harry's joy to discover that flying on a broomstick is something magical that he can do, not only naturally and well, but better than anyone else in the class. Compound this with the discovery that his father was also a talented flier, that he no longer has to attend flying classes with the Slytherins, that the school will be providing him with a top-quality broom for Quidditch matches—by dinner time, Harry could likely fly from sheer joy, without a broom.

Harry is also showing a growing independence by his tendency to break rules, almost from his first day at Hogwarts, as demonstrated by his ignoring Madam Hooch's command at the flying lesson that all students remain on the ground during her brief absence. Harry also sneaks out after curfew to meet Draco for their duel. This rule-breaking attitude may partially stem from his disdain for the Dursleys, who have constantly abused their authority to torment and unfairly punish Harry when he does nothing wrong, while Dudley is continually spoiled, despite his abysmal, bullying behavior. And even though Harry's nature is showing a certain disregard for authority, it is never motivated by rebellion or to engage in mischief; he instead feels justified if he believes his actions serve some noble purpose, such as retrieving Neville's Remembrall or upholding his honor by dueling Draco. In this instance, Harry's breaking the rules and demonstrating his natural skill at flying is rewarded rather than punished. This may serve to reinforce his tendency to ignore restrictions which he feels are unjustifiable.

Ron's following Harry to the Trophy Room for the midnight duel is the first time we have seen Ron breaking rules. We expect that, given the relationship between Harry and Ron, any further rule breaking by Ron will be from following Harry's lead rather than by Ron's own initiative. In contrast, Hermione, to Harry and Ron's continued annoyance, is the boys' polar opposite, memorizing and obeying every school rule, though rarely considering the logic behind them. While Hermione does nag at the other two when she catches them breaking regulations, we have not yet seen her report them to anyone. We do not yet understand why Hermione seems to have attached herself to Harry and Ron, but it could be surmised that she is trying to protect Gryffindor's reputation against the two troublemakers in her year group who may possibly lose House points due to their activities.

The wizards' duel, which may appear somewhat arbitrary, is a natural progression and says much about Harry's, Ron's, and Draco's characters; Draco has been humiliated, and therefore must have his revenge. And for Draco, betraying Harry (and, peripherally, Ron) to Filch would be as satisfying as defeating him, if he could, in a duel. It also lessens the risk he will be further humiliated – what if Harry actually beat him in a duel? Getting Filch to do his dirty work increases the chance that Harry will suffer, while effectively shielding Draco from the consequences, if any. Draco's cowardice is also glimpsed here, and it later lands him in more trouble than he can imagine. Unlike Draco, Harry shows courage and integrity by honoring his agreement to meet Draco at the appointed time. Ron also shows bravery and loyalty by offering to act as Harry's second. Not even Hermione's bossy threats will stop either boy from going, and, after getting herself locked out of Gryffindor, she instead resigns herself to tagging along, ostensibly to monitor their actions, but likely intrigued as well. Hermione's obsession with rules, and her threats to report the two boys, seem more bluff than actual substance, showing that her peers' opinions about her overrule her need to obey authority. Throughout the series, Hermione, though disapproving, will rarely interfere with the boys' activities, and her curiosity often compels her to trail along, and, eventually, join in. Regardless, neither Harry or Ron want her there, though her presence proves beneficial.

This scene also provides further evidence that there is a mystery for Harry to investigate. Harry already suspects that the grubby little package Hagrid brought back to Hogwarts is tied to the break-in at Gringotts. The students' midnight foray may have led them in the right direction to find it, if they come to believe that its necessary. Once again, Harry's rule breaking pays off when Hermione's keen observation notices the trap door in the third-floor corridor that the fierce, three-headed dog is apparently guarding.

Intermediate warning: Details follow which you may not wish to read at your current level.

The trap door under the three-headed dog is one among Hogwarts' many secrets foreshadowed in the previous chapter. The guarded hatch poses a huge question that needs to be answered: "What is under the trap door?" If the dog is guarding Hagrid's parcel, then one must question what else might lie beneath the castle's floors. Hogwarts holds many secrets for Harry to discover in this and also later books. Like the castle's shifting staircases, Harry must navigate a dangerous and ever-changing path before finding the answers.

The reader should remember that, at this point, Harry has no need to worry about what is in the parcel, or how it is guarded. The fact that it is likely under the trap door that the dog is guarding is an interesting bit of information, but of no use to Harry. However, over the course of this year, Harry's curiosity will drive him to try and find out exactly what was in the parcel, and he will determine that it is the Philosopher's Stone of the book title. At the same time, Harry will gradually become aware that others are seeking the Stone, either for their own benefit or in the hopes of re-animating Voldemort, and will attempt to warn the authorities of his worries. The authorities, notably Professor McGonagall, will disregard his warnings, and Harry will conclude that he alone can save the Stone. It is arguable whether he has reached the correct conclusion; however, in the end he will act and will successfully keep the Stone safe.

Although Harry's fears that his difficult Muggle upbringing has permanently damaged his magical abilities are generally groundless, this belief is not entirely invalid. Whatever their backgrounds, pure-blood, half-blood, or Muggle-born, young witches and wizards do have varying talents and levels of proficiencies, and these can be affected by their respective histories. Neville Longbottom, a pure-bred from a powerful wizard family, is particularly weak in magic. But rather than lacking talent or ability, he has been emotionally (and possibly physically) crippled by events in his life that are at least as traumatic as Harry's; this similarity of background becomes a factor that bonds the two boys. Harry is probably experiencing some early difficulties for similar reasons, as well as being insecure and new to magic, though he quickly overcomes these obstacles and catches up to his classmates; Neville, who may have been impaired by his well-meaning family's memory charms to alleviate trauma over his parents' tragic fates, will take longer to progress, though he does eventually develop into a competent wizard.

Hermione retreats from her threat to report Harry and Ron, and she will continue to overlook their constant rule-breaking in future books, even after she is appointed as a Gryffindor prefect. The only time she actually reports their activities to a teacher is in Harry Potter and the Prisoner of Azkaban. In that instance, she reports Harry to Professor McGonagall, not for any rule breaking, but because she was legitimately concerned for Harry's safety. Both Harry and Ron react angrily, however, shunning her for months, deeply hurting Hermione, and nearly ending their friendship permanently.

Draco chooses Crabbe as his second. This suggests that he believes Crabbe to be the more powerful wizard, and so albeit by a tenuous chain of circumstance, may foreshadow the fact that Crabbe will die in the last book, and the way he dies.

This is also the first time we see the Trophy Room. At this time, the location of the duel may seem unimportant, but the location serves as a puzzle piece Harry uses to solve the mystery he pursues in Harry Potter and the Chamber of Secrets.